From 968812a874c571249b3fb59fb352ce4cd385a18a Mon Sep 17 00:00:00 2001
From: Ansgar Philippsen <ansgar.philippsen@gmail.com>
Date: Wed, 25 Jul 2012 18:00:02 +0200
Subject: [PATCH] moved mol.Transform to geom
The Transform class was moved from the mol module to the geom module. A typedef
was put into the mol namespace in C++, and a similar alias was put into the
mol python module, with an added deprecation warning.
---
CMakeLists.txt | 7 +-
examples/code_fragments/dokk/ligand.py | 4 +-
examples/code_fragments/dokk/spnav_input.py | 2 +-
modules/geom/pymod/CMakeLists.txt | 1 +
.../base => geom}/pymod/export_transform.cc | 12 +-
modules/geom/pymod/wrap_geom.cc | 2 +
modules/geom/src/CMakeLists.txt | 3 +-
modules/geom/src/geom.hh | 1 +
modules/{mol/base => geom}/src/transform.cc | 49 +-----
modules/{mol/base => geom}/src/transform.hh | 84 +++++-----
modules/geom/tests/CMakeLists.txt | 1 +
.../base => geom}/tests/test_transform.cc | 7 +-
modules/img/alg/pymod/wrap_alg.cc | 153 +++++++++---------
modules/img/alg/tests/test_transform.cc | 15 +-
modules/info/pymod/wrap_info.cc | 4 +
modules/info/src/geom_info_conversion.cc | 33 +++-
modules/info/src/geom_info_conversion.hh | 9 ++
modules/mol/base/pymod/CMakeLists.txt | 1 -
modules/mol/base/pymod/__init__.py | 11 ++
modules/mol/base/pymod/wrap_mol.cc | 2 -
modules/mol/base/src/CMakeLists.txt | 3 +-
modules/mol/base/src/coord_group.hh | 7 +-
modules/mol/base/src/coord_source.hh | 5 +-
modules/mol/base/tests/CMakeLists.txt | 1 -
24 files changed, 213 insertions(+), 204 deletions(-)
rename modules/{mol/base => geom}/pymod/export_transform.cc (91%)
rename modules/{mol/base => geom}/src/transform.cc (78%)
rename modules/{mol/base => geom}/src/transform.hh (53%)
rename modules/{mol/base => geom}/tests/test_transform.cc (92%)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ba1c57dd6..1556db88d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -318,6 +318,9 @@ message(STATUS
" Compound Lib (-DCOMPOUND_LIB) : ${_COMP_LIB}\n"
" TMAlign and TMScore (-DCOMPILE_TMTOOLS) : ${_TM_TOOLS}\n"
" Static Libraries (-DENABLE_STATIC) : ${ENABLE_STATIC}\n"
- " Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}\n"
- " Hidden object visibility (-DHIDDEN_VISIBILITY) : ${_HIDDEN_VIS}")
+ " Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}")
+if (CMAKE_COMPILER_IS_GNUCXX)
+ message(STATUS
+ " Hidden object visibility (-DHIDDEN_VISIBILITY) : ${_HIDDEN_VIS}")
+endif()
diff --git a/examples/code_fragments/dokk/ligand.py b/examples/code_fragments/dokk/ligand.py
index 4fc297ebc..2683aaddb 100644
--- a/examples/code_fragments/dokk/ligand.py
+++ b/examples/code_fragments/dokk/ligand.py
@@ -100,7 +100,7 @@ class Ligand:
shift_vec = geom.Vec3(float(self.config.start["POSX"]),
float(self.config.start["POSY"]),
float(self.config.start["POSZ"]))
- transf = mol.Transform()
+ transf = geom.Transform()
transf.SetTrans(shift_vec)
edi.SetTransform(transf.GetMatrix())
self.RotateAxis(geom.Vec3(1,0,0), float(self.config.start["ROTX"]))
@@ -123,4 +123,4 @@ class Ligand:
if dot>0:
vec-=dot*p.GetNormal()
return vec
- return vec
\ No newline at end of file
+ return vec
diff --git a/examples/code_fragments/dokk/spnav_input.py b/examples/code_fragments/dokk/spnav_input.py
index e51798578..6f1a9de95 100644
--- a/examples/code_fragments/dokk/spnav_input.py
+++ b/examples/code_fragments/dokk/spnav_input.py
@@ -39,7 +39,7 @@ class SpnavInputDevice(QtCore.QObject):
def InputChanged(self, tx,ty,tz,rx,ry,rz):
if (not self._lock_input) and (self.level is not None):
ligand = self.level.ligand
- transf = mol.Transform()
+ transf = geom.Transform()
if(self.trans):
delta = geom.Vec3 ((tx/480.0)*self._trans_factor, (ty/480.0)*self._trans_factor, (-tz/480.0)*self._trans_factor)
transf.SetTrans(delta)
diff --git a/modules/geom/pymod/CMakeLists.txt b/modules/geom/pymod/CMakeLists.txt
index f79aeac4c..5988cc95b 100644
--- a/modules/geom/pymod/CMakeLists.txt
+++ b/modules/geom/pymod/CMakeLists.txt
@@ -14,6 +14,7 @@ set(OST_GEOM_PYMOD_SOURCES
export_composite2_op.cc
export_composite3_op.cc
export_quat.cc
+ export_transform.cc
)
if (NOT ENABLE_STATIC)
diff --git a/modules/mol/base/pymod/export_transform.cc b/modules/geom/pymod/export_transform.cc
similarity index 91%
rename from modules/mol/base/pymod/export_transform.cc
rename to modules/geom/pymod/export_transform.cc
index 1dc8bdc16..b2f921246 100644
--- a/modules/mol/base/pymod/export_transform.cc
+++ b/modules/geom/pymod/export_transform.cc
@@ -18,14 +18,10 @@
//------------------------------------------------------------------------------
#include <boost/python.hpp>
-#include <ost/mol/transform.hh>
-#if(OST_INFO_ENABLED)
-#include <ost/info/info.hh>
-#endif
+#include <ost/geom/transform.hh>
using namespace boost::python;
-using namespace ost;
-using namespace ost::mol;
+using namespace geom;
void export_Transform()
{
@@ -56,8 +52,4 @@ void export_Transform()
.def("ApplyZAxisTranslation",&Transform::ApplyZAxisTranslation)
.def("ApplyAxisRotation",&Transform::ApplyAxisRotation)
;
-#if(OST_INFO_ENABLED)
- def("TransformToInfo", &TransformToInfo);
- def("TransformFromInfo", &TransformFromInfo);
-#endif
}
diff --git a/modules/geom/pymod/wrap_geom.cc b/modules/geom/pymod/wrap_geom.cc
index 76bb79300..14df2fa8b 100644
--- a/modules/geom/pymod/wrap_geom.cc
+++ b/modules/geom/pymod/wrap_geom.cc
@@ -35,6 +35,7 @@ extern void export_Composite3();
extern void export_Composite2_op();
extern void export_Composite3_op();
extern void export_Quat();
+extern void export_Transform();
namespace details {
#if (defined(OST_STATIC_PROPERTY_WORKAROUND))
@@ -64,6 +65,7 @@ BOOST_PYTHON_MODULE(_ost_geom)
export_Composite2_op();
export_Composite3_op();
export_Quat();
+ export_Transform();
#if (defined(OST_STATIC_PROPERTY_WORKAROUND))
// workaround for a problem with boost python and python 2.6.3/4
diff --git a/modules/geom/src/CMakeLists.txt b/modules/geom/src/CMakeLists.txt
index b20b7d243..40f33282a 100644
--- a/modules/geom/src/CMakeLists.txt
+++ b/modules/geom/src/CMakeLists.txt
@@ -25,7 +25,7 @@ composite3_op.hh
aligned_cuboid.hh
vec_mat_predicates.hh
quat.hh
-
+transform.hh
point_cloud.hh
module_config.hh
)
@@ -43,6 +43,7 @@ composite3.cc
composite2_op.cc
composite3_op.cc
quat.cc
+transform.cc
aligned_cuboid.cc
point_cloud.cc
)
diff --git a/modules/geom/src/geom.hh b/modules/geom/src/geom.hh
index 138e8da92..2bf028ab5 100644
--- a/modules/geom/src/geom.hh
+++ b/modules/geom/src/geom.hh
@@ -29,5 +29,6 @@
#include "composite_op.hh"
#include "quat.hh"
#include "aligned_cuboid.hh"
+#include "transform.hh"
#endif
diff --git a/modules/mol/base/src/transform.cc b/modules/geom/src/transform.cc
similarity index 78%
rename from modules/mol/base/src/transform.cc
rename to modules/geom/src/transform.cc
index ba1e59258..d2a07f6ab 100644
--- a/modules/mol/base/src/transform.cc
+++ b/modules/geom/src/transform.cc
@@ -18,18 +18,13 @@
//------------------------------------------------------------------------------
#include <ost/config.hh>
-#if(OST_INFO_ENABLED)
-#include <ost/info/info.hh>
-#include <ost/info/geom_info_conversion.hh>
-#endif
#include <ost/log.hh>
-#include "transform.hh"
-
-namespace ost {
-using namespace geom;
+#include "transform.hh"
+#include "vecmat3_op.hh"
+#include "vecmat4_op.hh"
-namespace mol {
+namespace geom {
Transform::Transform():
rot_(Mat3(1,0,0, 0,1,0, 0,0,1)),
@@ -207,7 +202,7 @@ void Transform::update_tm()
try {
itm_ = Invert(tm_);
} catch (GeomException& e) {
- LOG_WARNING("caught GeomException in Transform::update_tm: " << e.what());
+ std::cerr << "caught GeomException in Transform::update_tm: " << e.what() << std::endl;
itm_=geom::Mat4();
}
}
@@ -221,36 +216,4 @@ void Transform::update_components()
trans_[2] = tm_(3,2);
}
-#if(OST_INFO_ENABLED)
-Transform TransformFromInfo(const info::InfoGroup& group)
-{
- if (!group.HasItem("center")) {
- throw info::InfoError("Error while loading transform from info: "
- "Group does not contain a center element");
- }
- if (!group.HasGroup("rotation")) {
- throw info::InfoError("Error while loading transform from info: "
- "Group does not contain a rotation element");
- }
- if (!group.HasItem("translation")) {
- throw info::InfoError("Error while loading transform from info: "
- "Group does not contain a translation element");
- }
- Transform tf;
- tf.SetCenter(group.GetItem("center").AsVector());
- tf.SetTrans(group.GetItem("translation").AsVector());
- tf.SetRot(info::Mat3FromInfo(group.GetGroup("rotation")));
- return tf;
-}
-
-void TransformToInfo(const Transform& transform, info::InfoGroup& group)
-{
- Transform tf;
- group.CreateItem("center", transform.GetCenter());
- group.CreateItem("translation", transform.GetTrans());
- info::InfoGroup rot=group.CreateGroup("rotation");
- info::Mat3ToInfo(transform.GetRot(), rot);
-}
-#endif
-
-}} // ns
+} // ns
diff --git a/modules/mol/base/src/transform.hh b/modules/geom/src/transform.hh
similarity index 53%
rename from modules/mol/base/src/transform.hh
rename to modules/geom/src/transform.hh
index f9c59f6f5..997f76395 100644
--- a/modules/mol/base/src/transform.hh
+++ b/modules/geom/src/transform.hh
@@ -16,37 +16,44 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#ifndef OST_MOL_BASE_TRANSFORM_HH
-#define OST_MOL_BASE_TRANSFORM_HH
+#ifndef OST_GEOM_TRANSFORM_HH
+#define OST_GEOM_TRANSFORM_HH
/*
Author: Ansgar Philippsen
*/
#include <ost/config.hh>
-#include <ost/geom/geom.hh>
-#if(OST_INFO_ENABLED)
-#include <ost/info/info_fw.hh>
-#endif
-#include <ost/mol/module_config.hh>
-namespace ost { namespace mol {
+#include "module_config.hh"
+#include "vec3.hh"
+#include "vec4.hh"
+#include "mat3.hh"
+#include "mat.hh"
+#include "aligned_cuboid.hh"
+
+namespace geom {
/// \brief basic and essential transformation class, including translation,
/// rotation and center of rotation
-class DLLEXPORT_OST_MOL Transform {
+class DLLEXPORT_OST_GEOM Transform {
public:
Transform();
- geom::Mat4 GetMatrix() const {return tm_;}
- geom::Mat4 GetTransposedMatrix() const {return ttm_;}
- geom::Mat4 GetInvertedMatrix() const {return itm_;}
+ /// \brief retrieve transformation matrix
+ Mat4 GetMatrix() const {return tm_;}
+ /// \brief retrieve transposed transformation matrix
+ Mat4 GetTransposedMatrix() const {return ttm_;}
+ /// \brief retrieve inverted transformation matrix
+ Mat4 GetInvertedMatrix() const {return itm_;}
- void SetCenter(const geom::Vec3& c);
- geom::Vec3 GetCenter() const;
+ /// \brief set center of rotation
+ void SetCenter(const Vec3& c);
+ /// \brief retrieve center of rotation
+ Vec3 GetCenter() const;
// directly set tm, messing up rot/trans/cen !
- void SetMatrix(const geom::Mat4& m);
+ void SetMatrix(const Mat4& m);
/// \name rotation
//@{
@@ -54,51 +61,40 @@ public:
void ApplyXAxisRotation(float delta);
void ApplyYAxisRotation(float delta);
void ApplyZAxisRotation(float delta);
- void ApplyAxisRotation(float delta, const geom::Vec3& axis);
+ void ApplyAxisRotation(float delta, const Vec3& axis);
- geom::Mat3 GetXAxisRotation(float delta);
- geom::Mat3 GetYAxisRotation(float delta);
- geom::Mat3 GetZAxisRotation(float delta);
+ Mat3 GetXAxisRotation(float delta);
+ Mat3 GetYAxisRotation(float delta);
+ Mat3 GetZAxisRotation(float delta);
- geom::Mat3 GetRot() const;
- void SetRot(const geom::Mat3& r);
+ Mat3 GetRot() const;
+ void SetRot(const Mat3& r);
//@}
/// \brief translation
//@{
void ApplyXAxisTranslation(float delta);
void ApplyYAxisTranslation(float delta);
void ApplyZAxisTranslation(float delta);
- void SetTrans(const geom::Vec3& t);
- geom::Vec3 GetTrans() const;
+ void SetTrans(const Vec3& t);
+ Vec3 GetTrans() const;
//@}
- geom::Vec3 Apply(const geom::Vec3& v) const;
- geom::Vec4 Apply(const geom::Vec4& v) const;
- geom::AlignedCuboid Apply(const geom::AlignedCuboid& c) const;
+ Vec3 Apply(const Vec3& v) const;
+ Vec4 Apply(const Vec4& v) const;
+ AlignedCuboid Apply(const AlignedCuboid& c) const;
private:
- geom::Mat3 rot_;
- geom::Vec3 trans_;
- geom::Vec3 cen_;
- geom::Mat4 tm_;
- geom::Mat4 ttm_;
- geom::Mat4 itm_;
+ Mat3 rot_;
+ Vec3 trans_;
+ Vec3 cen_;
+ Mat4 tm_;
+ Mat4 ttm_;
+ Mat4 itm_;
void update_tm();
void update_components();
};
-
-
-#if(OST_INFO_ENABLED)
-/// \brief read transformation from info group
-/// \relates Transform
-Transform DLLEXPORT_OST_MOL TransformFromInfo(const info::InfoGroup& group);
-/// \brief store transformation in info group
-/// \relates Transform
-void DLLEXPORT_OST_MOL TransformToInfo(const Transform& transform,
- info::InfoGroup& group);
-#endif
-}} // ns
+} // ns
#endif
diff --git a/modules/geom/tests/CMakeLists.txt b/modules/geom/tests/CMakeLists.txt
index 027a16749..e4056c278 100644
--- a/modules/geom/tests/CMakeLists.txt
+++ b/modules/geom/tests/CMakeLists.txt
@@ -11,6 +11,7 @@ set(GEOM_UNITTESTS
test_vec2.cc
test_vec3.cc
test_vec4.cc
+ test_transform.cc
tests.cc
test_geom.py
)
diff --git a/modules/mol/base/tests/test_transform.cc b/modules/geom/tests/test_transform.cc
similarity index 92%
rename from modules/mol/base/tests/test_transform.cc
rename to modules/geom/tests/test_transform.cc
index 5c950acc5..5f4a543fd 100644
--- a/modules/mol/base/tests/test_transform.cc
+++ b/modules/geom/tests/test_transform.cc
@@ -22,14 +22,11 @@
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/mol/mol.hh>
-#include <ost/mol/transform.hh>
#include <ost/geom/geom.hh>
-using namespace ost;
-using namespace ost::mol;
+using namespace geom;
-BOOST_AUTO_TEST_SUITE( mol_base );
+BOOST_AUTO_TEST_SUITE( geom_base );
BOOST_AUTO_TEST_CASE(test_transform)
{
diff --git a/modules/img/alg/pymod/wrap_alg.cc b/modules/img/alg/pymod/wrap_alg.cc
index c141fe113..7185f3402 100644
--- a/modules/img/alg/pymod/wrap_alg.cc
+++ b/modules/img/alg/pymod/wrap_alg.cc
@@ -54,7 +54,7 @@
using namespace ost;
using namespace ost::img;
-using namespace ost::img::alg;
+//using namespace ost::img::alg;
using namespace boost::python;
// fw decl
@@ -63,11 +63,8 @@ void export_Normalizer();
void export_Transcendentals();
void export_Polar();
-using namespace ost::img;
-using namespace ost::img::alg;
-
namespace {
-list get_histo_bins(const Histogram& hist) {
+list get_histo_bins(const alg::Histogram& hist) {
list result;
const std::vector<int>& bins = hist.GetBins();
for(std::vector<int>::const_iterator it=bins.begin();it!=bins.end();++it) {
@@ -76,32 +73,32 @@ list get_histo_bins(const Histogram& hist) {
return result;
}
-void frac_shift0(FractionalShift* s)
+void frac_shift0(alg::FractionalShift* s)
{
s->SetShift();
}
-void frac_shift1(FractionalShift* s, Real sx)
+void frac_shift1(alg::FractionalShift* s, Real sx)
{
s->SetShift(sx);
}
-void frac_shift2(FractionalShift* s, Real sx, Real sy)
+void frac_shift2(alg::FractionalShift* s, Real sx, Real sy)
{
s->SetShift(sx,sy);
}
-void frac_shift3(FractionalShift* s, Real sx, Real sy, Real sz)
+void frac_shift3(alg::FractionalShift* s, Real sx, Real sy, Real sz)
{
s->SetShift(sx,sy,sz);
}
-void frac_shift4(FractionalShift* s, const Vec2& v)
+void frac_shift4(alg::FractionalShift* s, const Vec2& v)
{
s->SetShift(v);
}
-void frac_shift5(FractionalShift* s, const Vec3& v)
+void frac_shift5(alg::FractionalShift* s, const Vec3& v)
{
s->SetShift(v);
}
@@ -109,7 +106,7 @@ void frac_shift5(FractionalShift* s, const Vec3& v)
Real real_spatial_cross_correlation_1(const ConstImageHandle& image1,
const ConstImageHandle& image2)
{
- return RealSpatialCrossCorrelation(image1,image2);
+ return alg::RealSpatialCrossCorrelation(image1,image2);
}
@@ -117,94 +114,94 @@ Real real_spatial_cross_correlation_2(const ConstImageHandle& image1,
const ConstImageHandle& image2,
const Extent& extent)
{
- return RealSpatialCrossCorrelation(image1,image2,extent);
+ return alg::RealSpatialCrossCorrelation(image1,image2,extent);
}
} //anon ns
BOOST_PYTHON_MODULE(_ost_img_alg)
{
- class_<AutoCorrelate, bases<ConstModOPAlgorithm> >("AutoCorrelate",init<>());
+ class_<alg::AutoCorrelate, bases<ConstModOPAlgorithm> >("AutoCorrelate",init<>());
- class_<Clear,bases<ConstModIPAlgorithm> >("Clear", init<>());
+ class_<alg::Clear,bases<ConstModIPAlgorithm> >("Clear", init<>());
- class_<Conj,bases<ConstModIPAlgorithm> >("Conj", init<>());
+ class_<alg::Conj,bases<ConstModIPAlgorithm> >("Conj", init<>());
- class_<ExplicitConvolute,bases<ConstModOPAlgorithm> >("ExplicitConvolute", init<const ConstImageHandle&,optional<bool> >());
+ class_<alg::ExplicitConvolute,bases<ConstModOPAlgorithm> >("ExplicitConvolute", init<const ConstImageHandle&,optional<bool> >());
- class_<ExplicitCorrelate,bases<ConstModOPAlgorithm> >("ExplicitCorrelate", init<const ConstImageHandle&>());
+ class_<alg::ExplicitCorrelate,bases<ConstModOPAlgorithm> >("ExplicitCorrelate", init<const ConstImageHandle&>());
- class_<CrossCorrelate,bases<ConstModIPAlgorithm> >("CrossCorrelate", init<const ConstImageHandle&>());
+ class_<alg::CrossCorrelate,bases<ConstModIPAlgorithm> >("CrossCorrelate", init<const ConstImageHandle&>());
- class_<DFT,bases<ConstModOPAlgorithm> >("DFT", init<>());
+ class_<alg::DFT,bases<ConstModOPAlgorithm> >("DFT", init<>());
- class_<FFT,bases<ConstModOPAlgorithm> >("FFT", init<>());
+ class_<alg::FFT,bases<ConstModOPAlgorithm> >("FFT", init<>());
- class_<PowerSpectrum,bases<ConstModOPAlgorithm> >("PowerSpectrum",init<>());
+ class_<alg::PowerSpectrum,bases<ConstModOPAlgorithm> >("PowerSpectrum",init<>());
- class_<Fill,bases<ConstModIPAlgorithm> >("Fill", init<const Complex&>())
+ class_<alg::Fill,bases<ConstModIPAlgorithm> >("Fill", init<const Complex&>())
.def(init<Real>())
;
- class_<Threshold,bases<ConstModIPAlgorithm> >("Threshold", init<const Complex&>())
+ class_<alg::Threshold,bases<ConstModIPAlgorithm> >("Threshold", init<const Complex&>())
.def(init<Real>())
;
- class_<DensitySlice,bases<ConstModIPAlgorithm> >("DensitySlice",
+ class_<alg::DensitySlice,bases<ConstModIPAlgorithm> >("DensitySlice",
init<const Complex&,const Complex&>())
.def(init<Real,Real>())
;
- class_<ClipMinMax,bases<ConstModIPAlgorithm> >("ClipMinMax",
+ class_<alg::ClipMinMax,bases<ConstModIPAlgorithm> >("ClipMinMax",
init<const Complex&,const Complex&>())
.def(init<Real,Real>())
;
- class_<Histogram, bases<NonModAlgorithm> >("Histogram", init<int,Real,Real>() )
+ class_<alg::Histogram, bases<NonModAlgorithm> >("Histogram", init<int,Real,Real>() )
.def("GetBins",get_histo_bins)
;
- class_<Negate,bases<ConstModIPAlgorithm> >("Negate", init<>());
-
- class_<Stat, bases<NonModAlgorithm> >("Stat", init<>() )
- .def("GetMean",&Stat::GetMean)
- .def("SetMean",&Stat::SetMean)
- .def("GetMinimum",&Stat::GetMinimum)
- .def("GetMinimumPosition",&Stat::GetMinimumPosition)
- .def("SetMinimum",&Stat::SetMinimum)
- .def("GetMaximum",&Stat::GetMaximum)
- .def("GetMaximumPosition",&Stat::GetMaximumPosition)
- .def("SetMaximum",&Stat::SetMaximum)
- .def("GetSum",&Stat::GetSum)
- .def("GetRootMeanSquare",&Stat::GetRootMeanSquare)
- .def("GetSkewness",&Stat::GetSkewness)
- .def("GetKurtosis",&Stat::GetKurtosis)
- .def("GetVariance",&Stat::GetVariance)
- .def("SetVariance",&Stat::SetVariance)
- .def("GetStandardDeviation",&Stat::GetStandardDeviation)
- .def("SetStandardDeviation",&Stat::SetStandardDeviation)
- .def("GetCenterOfMass",&Stat::GetCenterOfMass)
+ class_<alg::Negate,bases<ConstModIPAlgorithm> >("Negate", init<>());
+
+ class_<alg::Stat, bases<NonModAlgorithm> >("Stat", init<>() )
+ .def("GetMean",&alg::Stat::GetMean)
+ .def("SetMean",&alg::Stat::SetMean)
+ .def("GetMinimum",&alg::Stat::GetMinimum)
+ .def("GetMinimumPosition",&alg::Stat::GetMinimumPosition)
+ .def("SetMinimum",&alg::Stat::SetMinimum)
+ .def("GetMaximum",&alg::Stat::GetMaximum)
+ .def("GetMaximumPosition",&alg::Stat::GetMaximumPosition)
+ .def("SetMaximum",&alg::Stat::SetMaximum)
+ .def("GetSum",&alg::Stat::GetSum)
+ .def("GetRootMeanSquare",&alg::Stat::GetRootMeanSquare)
+ .def("GetSkewness",&alg::Stat::GetSkewness)
+ .def("GetKurtosis",&alg::Stat::GetKurtosis)
+ .def("GetVariance",&alg::Stat::GetVariance)
+ .def("SetVariance",&alg::Stat::SetVariance)
+ .def("GetStandardDeviation",&alg::Stat::GetStandardDeviation)
+ .def("SetStandardDeviation",&alg::Stat::SetStandardDeviation)
+ .def("GetCenterOfMass",&alg::Stat::GetCenterOfMass)
.def(self_ns::str(self))
;
- class_<StatMinMax, bases<NonModAlgorithm> >("StatMinMax", init<>() )
- .def("GetMinimum",&StatMinMax::GetMinimum)
- .def("GetMinimumPosition",&StatMinMax::GetMinimumPosition)
- .def("SetMinimum",&StatMinMax::SetMinimum)
- .def("GetMaximum",&StatMinMax::GetMaximum)
- .def("GetMaximumPosition",&StatMinMax::GetMaximumPosition)
- .def("SetMaximum",&StatMinMax::SetMaximum)
+ class_<alg::StatMinMax, bases<NonModAlgorithm> >("StatMinMax", init<>() )
+ .def("GetMinimum",&alg::StatMinMax::GetMinimum)
+ .def("GetMinimumPosition",&alg::StatMinMax::GetMinimumPosition)
+ .def("SetMinimum",&alg::StatMinMax::SetMinimum)
+ .def("GetMaximum",&alg::StatMinMax::GetMaximum)
+ .def("GetMaximumPosition",&alg::StatMinMax::GetMaximumPosition)
+ .def("SetMaximum",&alg::StatMinMax::SetMaximum)
.def(self_ns::str(self))
;
- class_<Randomize,bases<ConstModIPAlgorithm> >("Randomize", init<>());
+ class_<alg::Randomize,bases<ConstModIPAlgorithm> >("Randomize", init<>());
- class_<MaskImage, bases<ConstModIPAlgorithm> >("MaskImage",init<const MaskPtr&,optional<bool> >())
+ class_<alg::MaskImage, bases<ConstModIPAlgorithm> >("MaskImage",init<const MaskPtr&,optional<bool> >())
;
- class_<SmoothMaskImage, bases<ModIPAlgorithm> >("SmoothMaskImage",init<const MaskPtr&, Real, optional<bool> >())
+ class_<alg::SmoothMaskImage, bases<ModIPAlgorithm> >("SmoothMaskImage",init<const MaskPtr&, Real, optional<bool> >())
;
- class_<LocalSigmaThreshold, bases<ConstModOPAlgorithm> >("LocalSigmaThreshold", init<int,Real>() );
+ class_<alg::LocalSigmaThreshold, bases<ConstModOPAlgorithm> >("LocalSigmaThreshold", init<int,Real>() );
export_Filter();
export_Normalizer();
@@ -212,34 +209,34 @@ BOOST_PYTHON_MODULE(_ost_img_alg)
export_Transcendentals();
- class_<Transformation>("Transformation", init<>())
+ class_<alg::Transformation>("Transformation", init<>())
.def(init<const Mat4&>())
.def(init<const Mat4&, const Mat4&>())
;
- class_<Rotate2D, bases<Transformation> >("Rotate2D", init<Real>() );
- class_<Rotate2D90, bases<Transformation> >("Rotate2D90", init<int>() );
- class_<Scale, bases<Transformation> >("Scale", init<Real>() );
- class_<Translate, bases<Transformation> >("Translate", init<const Vec3&>() );
+ class_<alg::Rotate2D, bases<alg::Transformation> >("Rotate2D", init<Real>() );
+ class_<alg::Rotate2D90, bases<alg::Transformation> >("Rotate2D90", init<int>() );
+ class_<alg::Scale, bases<alg::Transformation> >("Scale", init<Real>() );
+ class_<alg::Translate, bases<alg::Transformation> >("Translate", init<const Vec3&>() );
- class_<Transform,bases<ConstModOPAlgorithm> >("Transform",init<>())
- .def(init<const Transformation&, optional<const Vec3&> >())
+ class_<alg::Transform,bases<ConstModOPAlgorithm> >("Transform",init<>())
+ .def(init<const alg::Transformation&, optional<const Vec3&> >())
;
- class_<Shift,bases<ConstModOPAlgorithm> >("Shift",init<>())
+ class_<alg::Shift,bases<ConstModOPAlgorithm> >("Shift",init<>())
.def(init<const Point&>())
;
- class_<Mirror,bases<ConstModOPAlgorithm> >("Mirror",init<>())
+ class_<alg::Mirror,bases<ConstModOPAlgorithm> >("Mirror",init<>())
.def(init<int>())
;
- class_<DiscreteShrink, bases<ConstModOPAlgorithm> >("DiscreteShrink",init<optional<const Size&> >())
- .def("SetBlocksize",&DiscreteShrink::SetBlocksize)
- .def("GetBlocksize",&DiscreteShrink::GetBlocksize)
+ class_<alg::DiscreteShrink, bases<ConstModOPAlgorithm> >("DiscreteShrink",init<optional<const Size&> >())
+ .def("SetBlocksize",&alg::DiscreteShrink::SetBlocksize)
+ .def("GetBlocksize",&alg::DiscreteShrink::GetBlocksize)
;
- class_<FractionalShift, bases<ModIPAlgorithm> >("FractionalShift", init<optional <Real,Real,Real> >() )
+ class_<alg::FractionalShift, bases<ModIPAlgorithm> >("FractionalShift", init<optional <Real,Real,Real> >() )
.def(init<const Vec3&>())
.def("SetShift",frac_shift0)
.def("SetShift",frac_shift1)
@@ -247,22 +244,22 @@ BOOST_PYTHON_MODULE(_ost_img_alg)
.def("SetShift",frac_shift3)
.def("SetShift",frac_shift4)
.def("SetShift",frac_shift5)
- .def("GetShift",&FractionalShift::GetShift)
+ .def("GetShift",&alg::FractionalShift::GetShift)
;
- class_<LineAverage, bases<ConstModOPAlgorithm> >("LineAverage", init<>() )
+ class_<alg::LineAverage, bases<ConstModOPAlgorithm> >("LineAverage", init<>() )
.def(init<unsigned int>())
- .def("GetGeometry",&LineAverage::GetGeometry)
- .def("SetGeometry",&LineAverage::SetGeometry)
+ .def("GetGeometry",&alg::LineAverage::GetGeometry)
+ .def("SetGeometry",&alg::LineAverage::SetGeometry)
;
def("RealSpatialCrossCorrelation",real_spatial_cross_correlation_1);
def("RealSpatialCrossCorrelation",real_spatial_cross_correlation_2);
- class_<HighestPeakSearch3D, bases<NonModAlgorithm> >("HighestPeakSearch3D" ,init<int,int,Real>())
+ class_<alg::HighestPeakSearch3D, bases<NonModAlgorithm> >("HighestPeakSearch3D" ,init<int,int,Real>())
.def(init<int,int>())
.def(init<int>())
.def(init<>())
- .def("GetPeakList",&HighestPeakSearch3D::GetPeakList)
- .def("ClearPeakList",&HighestPeakSearch3D::ClearPeakList)
+ .def("GetPeakList",&alg::HighestPeakSearch3D::GetPeakList)
+ .def("ClearPeakList",&alg::HighestPeakSearch3D::ClearPeakList)
;
}
diff --git a/modules/img/alg/tests/test_transform.cc b/modules/img/alg/tests/test_transform.cc
index 2721c3369..62a12549d 100644
--- a/modules/img/alg/tests/test_transform.cc
+++ b/modules/img/alg/tests/test_transform.cc
@@ -33,21 +33,20 @@
namespace {
using namespace ost::img;
-using namespace ost::img::alg;
void test()
{
alg::Randomize rnd;
- Transform transform;
+ alg::Transform transform;
}
void test_point()
{
Point p0(3,-2,1);
Point p1a(9,-6,3);
- Point p1b(Scale(3.0).Apply(p0));
+ Point p1b(alg::Scale(3.0).Apply(p0));
Point p2a(Point(2,3,1));
- Point p2b=Rotate2D(M_PI_2).Apply(p0);
+ Point p2b=alg::Rotate2D(M_PI_2).Apply(p0);
std::ostringstream msg;
msg << p1a << " != " << p1b;
@@ -61,9 +60,9 @@ void test_extent()
{
Extent e0(Point(0,0),Point(2,3));
Extent e1a(Point(-1,-1),Point(7,10));
- Extent e1b=Scale(3.0).Apply(e0);
+ Extent e1b=alg::Scale(3.0).Apply(e0);
Extent e2a(Point(-3,0),Point(0,2));
- Extent e2b=Rotate2D(M_PI_2).Apply(e0);
+ Extent e2b=alg::Rotate2D(M_PI_2).Apply(e0);
std::ostringstream msg;
msg << e1a << " != " << e1b;
@@ -74,10 +73,10 @@ void test_extent()
e0=Extent(Point(-3,-2),Size(8,10));
e1a=Extent(Point(-10,-7),Size(24,30));
- e1b=Scale(3.0).Apply(e0);
+ e1b=alg::Scale(3.0).Apply(e0);
e2a=Extent(Point(-7,-3),Size(10,8));
- e2b=Rotate2D(M_PI_2).Apply(e0);
+ e2b=alg::Rotate2D(M_PI_2).Apply(e0);
msg.str("");
msg << e1a << " != " << e1b;
diff --git a/modules/info/pymod/wrap_info.cc b/modules/info/pymod/wrap_info.cc
index 4af9741d6..cf15c736d 100644
--- a/modules/info/pymod/wrap_info.cc
+++ b/modules/info/pymod/wrap_info.cc
@@ -314,4 +314,8 @@ BOOST_PYTHON_MODULE(_ost_info)
class_<VerboseInfoVisitor, bases<InfoVisitor> >("VerboseInfoVisitor",init<>())
;
+
+ def("TransformToInfo", &TransformToInfo);
+ def("TransformFromInfo", &TransformFromInfo);
+
}
diff --git a/modules/info/src/geom_info_conversion.cc b/modules/info/src/geom_info_conversion.cc
index 8c7681be5..8e5711904 100644
--- a/modules/info/src/geom_info_conversion.cc
+++ b/modules/info/src/geom_info_conversion.cc
@@ -80,4 +80,35 @@ geom::Mat4 Mat4FromInfo(const InfoGroup& group)
return mat;
}
-}}
+geom::Transform TransformFromInfo(const InfoGroup& group)
+{
+ if (!group.HasItem("center")) {
+ throw InfoError("Error while loading transform from info: "
+ "Group does not contain a center element");
+ }
+ if (!group.HasGroup("rotation")) {
+ throw InfoError("Error while loading transform from info: "
+ "Group does not contain a rotation element");
+ }
+ if (!group.HasItem("translation")) {
+ throw InfoError("Error while loading transform from info: "
+ "Group does not contain a translation element");
+ }
+ geom::Transform tf;
+ tf.SetCenter(group.GetItem("center").AsVector());
+ tf.SetTrans(group.GetItem("translation").AsVector());
+ tf.SetRot(Mat3FromInfo(group.GetGroup("rotation")));
+ return tf;
+}
+
+void TransformToInfo(const geom::Transform& transform, InfoGroup& group)
+{
+ geom::Transform tf;
+ group.CreateItem("center", transform.GetCenter());
+ group.CreateItem("translation", transform.GetTrans());
+ InfoGroup rot=group.CreateGroup("rotation");
+ Mat3ToInfo(transform.GetRot(), rot);
+}
+
+}} // ns
+
diff --git a/modules/info/src/geom_info_conversion.hh b/modules/info/src/geom_info_conversion.hh
index cb06e05eb..bab90abec 100644
--- a/modules/info/src/geom_info_conversion.hh
+++ b/modules/info/src/geom_info_conversion.hh
@@ -53,6 +53,15 @@ void DLLEXPORT_OST_INFO Mat4ToInfo(const geom::Mat4& mat, InfoGroup& group);
///\brief load Mat4 from info
geom::Mat4 DLLEXPORT_OST_INFO Mat4FromInfo(const InfoGroup& group);
+
+/// \brief read transformation from info group
+/// \relates Transform
+geom::Transform DLLEXPORT_OST_INFO TransformFromInfo(const info::InfoGroup& group);
+/// \brief store transformation in info group
+/// \relates Transform
+void DLLEXPORT_OST_INFO TransformToInfo(const geom::Transform& transform,
+ info::InfoGroup& group);
+
//@}
}}
diff --git a/modules/mol/base/pymod/CMakeLists.txt b/modules/mol/base/pymod/CMakeLists.txt
index 6e158771a..3f514b2b8 100644
--- a/modules/mol/base/pymod/CMakeLists.txt
+++ b/modules/mol/base/pymod/CMakeLists.txt
@@ -18,7 +18,6 @@ export_bounding_box.cc
export_query_view_wrapper.cc
export_torsion.cc
export_visitor.cc
-export_transform.cc
wrap_mol.cc
export_entity_property_mapper.cc
)
diff --git a/modules/mol/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 8eb77fa6d..c51905578 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -20,6 +20,17 @@ from _ost_mol import *
import ost.geom as _geom
from ost.mol import alg
+__transform_warning_flag=True
+
+def Transform(tf=None):
+ from ost import LogWarning
+ if __transform_warning_flag:
+ LogWarning("mol.Transform is deprecated, please use geom.Transform instead")
+ __transform_warning_flag=False
+ if tf:
+ return _geom.Transform(tf)
+ else:
+ return _geom.Transform()
def MergeCoordGroups(*coord_groups):
"""
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index 31cf8165b..0c1281ad8 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -42,7 +42,6 @@ void export_PropertyID();
void export_BoundingBox();
void export_QueryViewWrapper();
void export_EntityPropertyMapper();
-void export_Transform();
BOOST_PYTHON_MODULE(_ost_mol)
{
@@ -71,5 +70,4 @@ BOOST_PYTHON_MODULE(_ost_mol)
export_BoundingBox();
export_QueryViewWrapper();
export_EntityPropertyMapper();
- export_Transform();
}
diff --git a/modules/mol/base/src/CMakeLists.txt b/modules/mol/base/src/CMakeLists.txt
index 7c92f9f45..8bb7187eb 100644
--- a/modules/mol/base/src/CMakeLists.txt
+++ b/modules/mol/base/src/CMakeLists.txt
@@ -31,7 +31,6 @@ residue_view.cc
surface_builder.cc
surface_handle.cc
torsion_handle.cc
-transform.cc
query_view_wrapper.cc
view_op.cc
coord_source.cc
@@ -87,13 +86,13 @@ surface_builder.hh
surface_handle.hh
surface_prop.hh
torsion_handle.hh
-transform.hh
query_view_wrapper.hh
view_op.hh
view_type_fw.hh
view_op.hh
xcs_editor.hh
bounding_box.hh
+transform.hh
module_config.hh)
foreach(_impl_src ${OST_MOL_IMPL_SOURCES})
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 74fffcb6c..573ab8ffb 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -28,9 +28,12 @@
#include "atom_handle.hh"
#include "coord_source.hh"
-namespace ost { namespace mol {
+namespace geom {
+ // we should really have fw headers...
+ class Transform;
+}
-class Transform;
+namespace ost { namespace mol {
/// \brief coordinate group, for trajectories and such
class DLLEXPORT_OST_MOL CoordGroupHandle {
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index a33162abc..51cfe0717 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -27,11 +27,14 @@
#include <ost/mol/coord_frame.hh>
#include <ost/mol/entity_handle.hh>
+namespace geom {
+ // we should really have fw headers...
+ class Transform;
+}
namespace ost { namespace mol {
class CoordSource;
-class Transform;
typedef boost::shared_ptr<CoordSource> CoordSourcePtr;
diff --git a/modules/mol/base/tests/CMakeLists.txt b/modules/mol/base/tests/CMakeLists.txt
index c29dc6adf..5085b0b10 100644
--- a/modules/mol/base/tests/CMakeLists.txt
+++ b/modules/mol/base/tests/CMakeLists.txt
@@ -10,7 +10,6 @@ set(OST_MOL_BASE_UNIT_TESTS
test_query.cc
test_surface.cc
test_residue.cc
- test_transform.cc
test_view.cc
test_view_op.cc
tests.cc
--
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